MarquesLab

peak_hom should be 48 like here: [M::ha_analyze_count] lowest: count[12] = 9592695 [M::ha_analyze_count] highest: count[23] = 10879667 [M::ha_hist_line] 2: ****************************************************************************************************> 37164030 [M::ha_hist_line] 3: ****************************************************************************************************> 21995283 [M::ha_hist_line] 4: ****************************************************************************************************> 19267091 [M::ha_hist_line] 5:...

What would be small -s? I have tried -s 0.1, but it did not really improve. I will try together with --hom-cov 48

That's the thing. I am running from a cluster with 500G RAM and 64 threads

Thanks! I will try on our HPC cluster with 1TB or adjust the parameters as you suggested. How long should the whole run take? I am not sure is a...

somehow is strange... running on our HPC node with 1TB the job exits with> Resource usage summary: CPU time : 2301.09 sec. Max Memory : 69212 MB Max Swap :...

We use LSF, but I set the memory limit to 980G, and still exits. But it seems that the max memory set was not even reached before it exits.

it did advance a bit, but still failed. 24-02-04 08:21:52 [INFO] Loading /netscratch/dep_mercier/grp_marques/marques/LPA/CBC/SubPhaser/wgdi/non-necessary/CBC_tmp/CBC_chromosomes/scaffold_19.fasta_15.fa 24-02-04 08:22:07 [INFO] Loading /netscratch/dep_mercier/grp_marques/marques/LPA/CBC/SubPhaser/wgdi/non-necessary/CBC_tmp/CBC_chromosomes/scaffold_20.fasta_15.fa 24-02-04 08:22:19 [INFO] Loading /netscratch/dep_mercier/grp_marques/marques/LPA/CBC/SubPhaser/wgdi/non-necessary/CBC_tmp/CBC_chromosomes/scaffold_45.fasta_15.fa 24-02-04 08:22:31 [INFO] Loading /netscratch/dep_mercier/grp_marques/marques/LPA/CBC/SubPhaser/wgdi/non-necessary/CBC_tmp/CBC_chromosomes/scaffold_46.fasta_15.fa 24-02-04 08:22:41...

Ok, thanks a lot for the suggestion. I have finally managed to run SubPhaser using the unphased genome version and as initially suspected, I guess it looks pretty much like...

Thanks a lot! It just worked perfect! Is there a way I can specify the color to each subgenome? You should receive a nobel for that tool. So awesome!

just found the right commands, please ignore the message above, but the nobel thing still holds true :-)